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PubMed2025

Latent preference for red ornamentation drives interspecific mating in nascent jumping spider species (Habronattus americanus group, F. Salticidae).

Heterospecific interactions between nascent species offer insights into how sexual selection shapes novel traits, illuminating patterns in species interactions and diversification. We tested female preferences between two recently diverged, allopatric species of jumping spiders: Habronattus americanus PLC, with red-coloured males performing short multimodal displays, and Habronattus sansoni CC, with brown-coloured males performing long multimodal displays. Mate choice experiments showed that females of both species preferred H. americanus PLC males. To examine the role of red coloration, we manipulated male coloration in both species. Results indicated that red-painted H. sansoni CC males experienced an increase in mating success, whereas brown-painted H. americanus PLCmales did not show reduced success. Our study suggests that (i) strong latent female preferences can drive unidirectional introgression across species boundaries, potentially leading to genomic homogenization; (ii) latent preferences may override preferences for existing traits; and (iii) the geographical distribution of colour morphs is consistent with a hypothesis of strong latent preferences across populations. Overall, our study demonstrates the role that mating interactions can play in speciation dynamics.

Animals↗

PubMed2025

Genomic signature and evolutionary history of completely cleistogamous lineages in the non-photosynthetic orchid Gastrodia.

Despite a long-standing interest since Darwin's time, the genomic implications of obligate self-fertilization remain elusive. Complete cleistogamy-the obligate production of closed, self-pollinating flowers-represents an extreme reproductive strategy. Here, we present the genomic profiles and evolutionary history of two lineages of the mycoheterotrophic orchid Gastrodia, both of which independently acquired complete cleistogamy, based on detailed sampling and a combination of simple sequence repeat (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq) and RNA-seq data. Our analysis reveals clear species delimitation, with no evidence of introgression between the completely cleistogamous species and their co-occurring allogamous sisters. Intriguingly, all analyses indicate that both the completely cleistogamous Gastrodia species and their allogamous sisters exhibit genetic profiles typical of self-pollinating plants. This pattern suggests that their ancestors, probably bearing allogamous flowers, had already evolved mechanisms to mitigate the deleterious effects of selfing, potentially facilitating the emergence of complete cleistogamy through benefits such as reproductive assurance, enhanced colonization ability and species reinforcement. Meanwhile, further analyses suggest that complete cleistogamy evolved very recently (possibly within the last 1000-2000 years) in these two Gastrodia lineages. Combined with the scant evidence of complete cleistogamy outside Gastrodia, our findings imply a limited and ephemeral role for complete cleistogamy in plant speciation.

Biological Evolution↗

PubMed2005

Selection in backcross programmes.

Backcrossing is a well-known and long established breeding scheme where a characteristic is introgressed from a donor parent into the genomic background of a recurrent parent. The various uses of backcrossing in modern genetics, particularly with the help of molecular markers, are reviewed here. Selection in backcross programmes is used to either improve the genetic value of plant and animal populations or fine map quantitative trait loci. Both cases are helpful in our understanding of the genetic bases of quantitative traits variation.

Animals↗

PubMed2005

DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.

DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.

Animals↗

PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Journal Article↗

PubMed2001

QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane.

QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31 different probes were found in two interspecific F(1) populations. Most QTL alleles showed phenotypic effects consistent with the parental phenotypes, but occasional transgressive QTLs revealed opportunities to purge unfavorable alleles from cultivars or introgress valuable alleles from exotics. Several QTLs on homologous chromosomes appeared to correspond to one another-multiple doses of favorable 'alleles' at such chromosomal region(s) yielded diminishing returns-such negative epistasis may contribute to phenotypic buffering. Fewer sugar content QTLs were discovered from the highest-sugar genotype than from lower-sugar genotypes, perhaps suggesting that many favorable alleles have been fixed by prior selection, i.e. that the genes for which allelic variants (QTLs) persist in improved sugarcanes may be a biased subset of the population of genes controlling sugar content. Comparison of these data to mutations and QTLs previously mapped in maize hinted that seed and biomass crops may share a partly-overlapping basis for genetic variation in carbohydrate deposition. However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues.

Alleles↗

PubMed2004

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments.

Dense coverage of the rice genome with polymorphic DNA markers is an invaluable tool for DNA marker-assisted breeding, positional cloning, and a wide range of evolutionary studies. We have aligned drafts of two rice subspecies, indica and japonica, and analyzed levels and patterns of genetic diversity. After filtering multiple copy and low quality sequence, 408,898 candidate DNA polymorphisms (SNPs/INDELs) were discerned between the two subspecies. These filters have the consequence that our data set includes only a subset of the available SNPs (in particular excluding large numbers of SNPs that may occur between repetitive DNA alleles) but increase the likelihood that this subset is useful: Direct sequencing suggests that 79.8% +/- 7.5% of the in silico SNPs are real. The SNP sample in our database is not randomly distributed across the genome. In fact, 566 rice genomic regions had unusually high (328 contigs/48.6 Mb/13.6% of genome) or low (237 contigs/64.7 Mb/18.1% of genome) polymorphism rates. Many SNP-poor regions were substantially longer than most SNP-rich regions, covering up to 4 Mb, and possibly reflecting introgression between the respective gene pools that may have occurred hundreds of years ago. Although 46.2% +/- 8.3% of the SNPs differentiate other pairs of japonica and indica genotypes, SNP rates in rice were not predictive of evolutionary rates for corresponding genes in another grass species, sorghum. The data set is freely available at http://www.plantgenome.uga.edu/snp.

Breeding↗

PubMed1996

A comprehensive map of the porcine genome.

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Animals↗

PubMed1998

Genome scan and congenic strains for blood pressure QTL using Dahl salt-sensitive rats.

An F2 population (n = 151) derived from Dahl salt-sensitive (S) and Lewis rats was raised on a 8% NaCl diet for 9 weeks and analyzed for blood pressure quantitative trait loci (QTL) by use of a whole genome scan. Chromosomes 5 and 10 yielded lod scores for linkage to blood pressure that were significant; chromosomes 1, 2, 3, 8, 16, 17, and 18 gave lod scores suggestive for linkage. Chromosome 7 gave a significant signal for heart weight with a lesser effect on blood pressure. Congenic strains were constructed by introgressing Lewis low-blood-pressure QTL alleles for chromosomes 1, 5, 10, and 17 into the S genetic background. Congenic strains for chromosomes 1, 5, and 10 had significantly lower blood pressure than S, proving the existence of QTL on these chromosomes, but the chromosome 17 congenic strain failed to trap a contrasting QTL allele. The QTL allele increasing blood pressure originated from S rats for all QTL except those on chromosomes 2 and 7 in which the Lewis allele increased blood pressure. Interactions between each QTL and every other locus in the genome scan yielded significant interactions between chromosomes 10 and 4, and between chromosomes 2 and 3.

Animals↗

PubMed2004

Maize starch-branching enzyme isoforms and amylopectin structure. In the absence of starch-branching enzyme IIb, the further absence of starch-branching enzyme Ia leads to increased branching.

Previous studies indicated that the deficiency of starch-branching enzyme (SBE) Ia in the single mutant sbe1a::Mu (sbe1a) has no impact on endosperm starch structure, whereas the deficiency of SBEIIb in the ae mutant is well known to reduce the branching of starch. We hypothesized that in maize (Zea mays) endosperm, the function of SBEIIb is predominant to that of SBEIa, and SBEIa would have an observable effect only on amylopectin structure in the absence of SBEIIb. To test this hypothesis, the mutant sbe1a was introgressed into lines containing either wx (lacking the granule-bound starch synthase GBSSI) or ae wx (lacking both SBEIIb and GBSSI) in the W64A background. Both western blotting and zymogram analysis confirmed the SBEIa deficiency in sbe1a wx and sbe1a ae wx, and the SBEIIb deficiency in ae wx and sbe1a ae wx. Using zymogram analysis, no pleiotropic effects of sbe1a genes on SBEIIa, starch synthase, or starch-debranching enzyme isoforms were observed. High-performance size exclusion chromatography analysis shows that the chain-length profiles of amylopectin as well as beta-limit dextrin were indistinguishable between wx and sbe1a wx, whereas significant differences for both were observed between ae wx and sbe1a ae wx, suggesting an effect of SBEIa on amylopectin biosynthesis that is observable only in the absence of SBEIIb. The amylopectin branch density and the average number of branches per cluster were both higher in endosperm starch from sbe1a ae wx than from ae wx. These results indicate possible functional interactions between SBE isoforms that may involve enzymatic inhibition. Both the cluster repeat distance and the distance between branch points on the short intracluster chains were similar for all genotypes however, suggesting a similar pattern of individual SBE isoforms in cluster initiation and the determination of branch point location.

1,4-alpha-Glucan Branching Enzyme↗

PubMed2000

Specific combinations of zein genes and genetic backgrounds influence the transcription of the heavy-chain zein genes in maize opaque-2 endosperms.

The transcript levels of heavy-chain zein genes (zH1 and zH2) and the occurrence of the zH polypeptides in different opaque-2 (o2) lines were investigated by RNA-blot analyses and by sodium dodecylsulfate-polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis protein fractionations. Four mutant alleles o2R, o2T, o2It, and o2-676 introgressed into different genetic backgrounds (GBs) were considered. The mono-dimensional gel electrophoresis zein pattern can be either conserved or different among the various GBs carrying the same o2 allele. Likewise, in the identical GB carrying different o2 alleles, the zein pattern can be either conserved or differentially affected by the different mutant allele. Zein protein analysis of reciprocal crosses between lines with different o2 alleles or the same o2 showed in some case a more than additive zH pattern in respect to the o2 parent lines. Electrophoretic mobility shift assay approaches, with O2-binding oligonucleotide and endosperm extracts from the above o2 lines, failed to reveal o2-specific retarded band in any of the o2 extracts. The results suggest that the promoter of some zH1 and zH2 contains motif(s) that can respond to factors other than O2.

Alleles↗

PubMed2004

Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.

Plant recognition of pathogen-derived molecules influences attack and counterattack strategies that affect the outcome of host-microbe interactions. To ascertain the global framework of host gene expression during biotrophic pathogen invasion, we analyzed in parallel the mRNA abundance of 22,792 host genes throughout 36 (genotype x pathogen x time) interactions between barley (Hordeum vulgare) and Blumeria graminis f. sp hordei (Bgh), the causal agent of powdery mildew disease. A split-split-plot design was used to investigate near-isogenic barley lines with introgressed Mla6, Mla13, and Mla1 coiled-coil, nucleotide binding site, Leu-rich repeat resistance alleles challenged with Bgh isolates 5874 (AvrMla6 and AvrMla1) and K1 (AvrMla13 and AvrMla1). A linear mixed model analysis was employed to identify genes with significant differential expression (P value < 0.0001) in incompatible and compatible barley-Bgh interactions across six time points after pathogen challenge. Twenty-two host genes, of which five were of unknown function, exhibited highly similar patterns of upregulation among all incompatible and compatible interactions up to 16 h after inoculation (hai), coinciding with germination of Bgh conidiospores and formation of appressoria. By contrast, significant divergent expression was observed from 16 to 32 hai, during membrane-to-membrane contact between fungal haustoria and host epidermal cells, with notable suppression of most transcripts identified as differentially expressed in compatible interactions. These findings provide a link between the recognition of general and specific pathogen-associated molecules in gene-for-gene specified resistance and support the hypothesis that host-specific resistance evolved from the recognition and prevention of the pathogen's suppression of plant basal defense.

Carrier Proteins↗

PubMed1999

Gnarley1 is a dominant mutation in the knox4 homeobox gene affecting cell shape and identity.

Maize leaves have a stereotypical pattern of cell types organized into discrete domains. These domains are altered by mutations in knotted1 (kn1) and knox (for kn1-like homeobox) genes. Gnarley (Gn1) is a dominant maize mutant that exhibits many of the phenotypic characteristics of the kn1 family of mutants. Gn1 is unique because it changes parameters of cell growth in the basal-most region of the leaf, the sheath, resulting in dramatically altered sheath morphology. The strongly expressive allele Gn1-R also gives rise to a floral phenotype in which ectopic carpels form. Introgression studies showed that the severity of the Gn1-conferred phenotype is strongly influenced by genetic background. Gn1 maps to knox4, and knox4 is ectopically expressed in plants with the Gn1-conferred phenotype. Immunolocalization experiments showed that the KNOX protein accumulates at the base of Gn1 leaves in a pattern that is spatially and temporally correlated with appearance of the mutant phenotype. We further demonstrate that Gn1 is knox4 by correlating loss of the mutant phenotype with insertion of a Mutator transposon into knox4.

Alleles↗

PubMed2000

Frequency and spatial patterning of clonal reproduction in Louisiana iris hybrid populations.

The plant genera in which natural hybridization is most prevalent tend to be outcrossing perennials with some mechanism for clonal (i.e., asexual) reproduction. Although clonal reproduction in fertile, sexually reproducing hybrid populations could have important evolutionary consequences, little attention has been paid to quantifying this parameter in such populations. In the present study, we examined the frequency and spatial patterning of clonal reproduction in two Louisiana iris hybrid populations. Allozyme analysis of both populations revealed relatively high levels of genotypic diversity. However, a considerable amount of clonality was apparent. Nearly half of all genets (47%) in one population and more than half (61%) in the other had multiple ramets. Furthermore, both populations exhibited relatively high levels of genetic structuring, a pattern that resulted from the aggregation of clonal ramets. The occurrence of clonal reproduction in hybrid populations could not only facilitate introgression through an increase in the number of flowering ramets per genet and/or the survivorship of early generation hybrids, but might also influence the mating system of such populations. Any potential increase in the selfing rate due to cross-pollination among ramets of the same genet may, in turn, increase the likelihood of homoploid hybrid speciation.

Biological Evolution↗

PubMed2000

Close genetic similarity between two sympatric species of tephritid fruit fly reproductively isolated by mating time.

Two sibling species of tephritid fruit fly, Bactrocera tryoni and B. neohumeralis, occur sympatrically throughout the range of B. neohumeralis in Australia. Isolation between the two species appears to be maintained by a difference in mating time: B. tryoni mates at dusk, whereas B. neohumeralis mates during the middle of the day. A morphological difference in humeral callus color also distinguishes the two species. Despite clear phenotypic evidence that B. tryoni and B. neohumeralis are distinct species, genetic differentiation as measured by four markers--nuclear DNA sequences from the white gene and the ribosomal internal transcribed spacer (ITS2), and mitochondrial DNA sequences from the cytochrome b (cytb) and cytochrome oxidase subunit II (COII) genes--is very small. Minor fixed differences occur in the ITS2 sequence, however, in all other cases the two species exhibit a high level of shared polymorphic variation. The close genetic similarity suggests either that speciation has occurred very rapidly and recently in the absence of any mitochondrial DNA sorting or that the sharing of polymorphisms is due to hybridization or introgression. A third species within the tryoni complex, B. aquilonis, is geographically isolated. Bactrocera aquilonis is also genetically very similar, but in this case there is clear differentiation for the mitochondrial loci. The three species form a group of considerable interest for investigation of speciation mechanisms.

Amino Acid Sequence↗

PubMed2001

Pollen- versus seed-mediated gene flow in a scattered forest tree species.

We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (G(STc) = 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen- nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

Chloroplasts↗

PubMed2001

Hybrid zone dynamics and species replacement between Orconectes crayfishes in a northern Wisconsin lake.

Hybrid zones that result in the genetic assimilation (replacement) of one species by another are underrepresented in the animal literature, most likely due to their transient nature. One such zone involves the rusty crayfish, Orconectes rusticus, and its congener O. propinquus. Orconectes rusticus was recently introduced into northern Wisconsin and Michigan lakes and streams, where it is hybridizing with and displacing resident O. propinquus. Here we report on a study investigating the dynamics of a hybrid zone between the two crayfish in Trout Lake, Wisconsin, where both the time (circa 1979) and location of the initial introduction are known. Our prediction was that hybridization should hasten the demise of O. propinquus because we expected that male O. rusticus (which are larger than congeners) would outcompete male O. propinquus for mates of both species. If hybrid progeny are unfit, then the result would be decreased reproductive output of O. propinquus females. However, we found a pattern of cytonuclear disequilibrium between allozymes and mtDNA suggesting that a majority (94.5%) of F1 hybrids resulted from matings between O. rusticus females and O. propinquus males. Also contrary to expectations, fecundity (O. rusticus and O. propinquus) and early hybrid survivorship did not differ significantly from nonhybrids. Moreover, adults of mixed ancestry were superior to both O. rusticus and O. propinquus in competition for a limiting food resource. Using a single-locus model, we estimated that hybridization increases the advance of O. rusticus genes in Trout Lake between 4.8% and 36.3% above that due to the previously documented ecological interactions. Consequently, whereas hybridization may be hastening the elimination of genetically pure O. propinquus, introgression is nevertheless slowing the loss of O. propinquus nuclear genes. Although our results suggest that O. rusticus and O. propinquus may not be true species under the biological concept, their ecological differences are of great conservation importance.

Animals↗

PubMed2001

Hybridization and population genetics of two macaque species in Sulawesi, Indonesia.

This study investigates hybridization and population genetics of two species of macaque monkey in Sulawesi, Indonesia, using molecular markers from mitochondrial, autosomal, and Y-chromosome DNA. Hybridization is the interbreeding of individuals from different parental taxa that are distinguishable by one or more heritable characteristics. Because hybridization can affect population structure of the parental taxa, it is an important consideration for conservation management. On the Indonesian island of Sulawesi an explosive diversification of macaques has occurred; seven of 19 species in the genus Macaca live on this island. The contact zone of the subjects of this study, M. maura and M. tonkeana, is located at the base of the southwestern peninsula of Sulawesi. Land conversion in Sulawesi is occurring at an alarming pace; currently two species of Sulawesi macaque, one of which is M. maura, are classified as endangered species. Results of this study indicate that hybridization among M. maura and M. tonkeana has led to different distributions of molecular variation in mitochondrial DNA and nuclear DNA in the contact zone; mitochondrial DNA shows a sharp transition from M. maura to M. tonkeana haplotypes, but nuclear DNA from the parental taxa is homogenized in a narrow hybrid zone. Similarly, within M. maura divergent mitochondrial DNA haplotypes are geographically structured but population subdivision in the nuclear genome is low or absent. In M. tonkeana, mitochondrial DNA haplotypes are geographically structured and a high level of nuclear DNA population subdivision is present in this species. These results are largely consistent with a macaque behavioral paradigm of female philopatry and obligate male dispersal, suggest that introgression between M. maura and M. tonkeana is restricted to the hybrid zone, and delineate one conservation management unit in M. maura and at least two in M. tonkeana.

Animals↗